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Complex sequence organization of heterochromatin in the holocentric plant Cuscuta europaea elucidated by the computational analysis of nanopore reads

SYSNO ASEP	0548344
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	Complex sequence organization of heterochromatin in the holocentric plant Cuscuta europaea elucidated by the computational analysis of nanopore reads
Author(s)	Vondrak, Tihana (BC-A)_RID Oliveira, Ludmila (BC-A)_{RID, ORCID} Novák, Petr (BC-A)_{RID, ORCID} Koblížková, Andrea (BC-A) Neumann, Pavel (BC-A)_{RID, ORCID} Macas, Jiří (BC-A)_{RID, ORCID, SAI}
Number of authors	6
Source Title	Computational and Structural Biotechnology Journal. - : Elsevier - ISSN 2001-0370 Roč. 19, Apr 22 (2021), s. 2179-2189
Number of pages	11 s.
Language	eng - English
Country	SE - Sweden
Keywords	Satellite DNA ; Heterochromatin ; Oxford Nanopore sequencing ; Fluorescence in situ hybridization ; Holocentric chromosomes ; LINE elements
Subject RIV	EB - Genetics ; Molecular Biology
OECD category	Genetics and heredity (medical genetics to be 3)
R&D Projects	GA20-24252S GA ČR - Czech Science Foundation (CSF)
	LM2018131 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
Research Infrastructure	ELIXIR-CZ II - 90131 - Ústav organické chemie a biochemie AV ČR, v. v. i.
Method of publishing	Open access
Institutional support	BC-A - RVO:60077344
UT WOS	000684934600009
EID SCOPUS	85104729200
DOI	10.1016/j.csbj.2021.04.011
Annotation	Repeat-rich regions of higher plant genomes are usually associated with constitutive heterochromatin, a specific type of chromatin that forms tightly packed nuclear chromocenters and chromosome bands. There is a large body of cytogenetic evidence that these chromosome regions are often composed of tandemly organized satellite DNA. However, comparatively little is known about the sequence arrangement within heterochromatic regions, which are difficult to assemble due to their repeated nature. Here, we explore long-range sequence organization of heterochromatin regions containing the major satellite repeat CUS-TR24 in the holocentric plant Cuscuta europaea. Using a combination of ultra-long read sequencing with assembly-free sequence analysis, we reveal the complex structure of these loci, which are composed of short arrays of CUS-TR24 interrupted frequently by emerging simple sequence repeats and targeted insertions of a specific lineage of LINE retrotransposons. These data suggest that the organization of satellite repeats constituting heterochromatic chromosome bands can be more complex than previously envisioned, and demonstrate that heterochromatin organization can be efficiently investigated without the need for genome assembly. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
Workplace	Biology Centre (since 2006)
Contact	Dana Hypšová, eje@eje.cz, Tel.: 387 775 214
Year of Publishing	2022
Electronic address	https://www.sciencedirect.com/science/article/pii/S2001037021001227?via%3Dihub

Number of the records: 1